QTL detection and candidate gene identification for prostrate growth habit in interspecific crosses of wild chrysanthemum (Chrysanthemum yantaiense × C. indicum)

Abstract

The prostrate growth habit is an important ornamental trait in ground-cover chrysanthemum, offering high aesthetic value, strong lodging resistance, and excellent landscape greening capability. However, the genetic basis underlying this trait in chrysanthemum remains largely unclear. In this study, we utilized the prostrate-type Chrysanthemum yantaiense (tetraploid), the erect-type C. indicum (tetraploid), and their 199 F₁ hybrid progenies to construct a high-density genetic linkage map through genotyping-by-sequencing. The biparental linkage maps included 4614 and 5180 SNP markers, with an average marker distance of 0.84 and 0.73 cM, respectively. After four years of phenotypic evaluation and one year of dynamic trait measurement in progenies for traits related to prostrate growth habit, we confirmed a stable quantitative trait locus (QTL) located on LG1-1 among co-localized QTLs using KASP markers. This QTL explained up to 20.13% of the phenotypic variation. As a result, a total of 44 genes were identified as candidate due to their tightly linkage with the peak QTL marker, Tag16173. Further phytohormone measurement, gene expression analysis, and transgenic studies confirmed that one of these candidates, the D type cyclin-encoding gene CyCYCD3;1, played a key role in the formation of prostrate growth habit in C. yantaiense. Our results not only enhance the understanding of the molecular mechanisms behind prostrate growth habit but also provide valuable molecular markers for improving plant architecture-related traits in chrysanthemum breeding.

Acknowledgments

This study was supported by the Science and Technology Innovation Program of Xiongan New Area (2022XAGG0100) and the National Natural Science Foundation of China (32271947).

Author contributions

D.W.L. and M.S. conceived and designed the project. M.S. and X.H.F. provided guidance for experimental design. D.W.L., Y.X.X., T.J.Z., H.L., and Y.Y.C. collected all materials and phenotypic data. D.W.L. constructed the genetic map. D.W.L. performed functional gene verification with assistance of Y.X.X., Y.L.L., Y.X.W., and Z.Y.G., D.W.L., and Y.X.X. performed the data analysis. D.W.L. and X.H.F. wrote the manuscript. M.S., X.H.F., and Y.C.T. revised and finalized the manuscript. All authors approved the manuscript before submission.

Data availability

All the data can be found in the main text or the supplements. The raw sequencing data of the population reported in this paper have been deposited in the NCBI BioProject under accession number PRJNA1214410.

Conflict of interest statement

The authors declare no conflict of interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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